Converter Script: `lsf2slurm.sh`¶

We provide a helper script that automates the most common LSF-to-SLURM conversions. It's located at scripts/lsf2slurm.sh in this repository.

Usage¶

# Convert a script (prints to stdout)
bash scripts/lsf2slurm.sh myjob.lsf

# Save the output to a new file
bash scripts/lsf2slurm.sh myjob.lsf > myjob.slurm

# Or redirect in place (use with caution)
bash scripts/lsf2slurm.sh myjob.sh > myjob_slurm.sh

What it converts¶

The script handles these substitutions:

Directives¶

LSF	SLURM
`#BSUB -J name`	`#SBATCH --job-name=name`
`#BSUB -q queue`	`#SBATCH --partition=queue`
`#BSUB -W HH:MM`	`#SBATCH --time=HH:MM:00`
`#BSUB -n N`	`#SBATCH --ntasks=N`
`#BSUB -M mem`	`#SBATCH --mem=memMB`
`#BSUB -o file`	`#SBATCH --output=file`
`#BSUB -e file`	`#SBATCH --error=file`
`#BSUB -N`	`#SBATCH --mail-type=END`
`#BSUB -B`	`#SBATCH --mail-type=BEGIN`
`#BSUB -u email`	`#SBATCH --mail-user=email`
`#BSUB -P project`	`#SBATCH --account=project`

Output filename tokens¶

LSF	SLURM
`%J`	`%j`
`%I`	`%a`

Environment variables¶

LSF	SLURM
`$LSB_JOBID`	`$SLURM_JOB_ID`
`$LSB_JOBINDEX`	`$SLURM_ARRAY_TASK_ID`
`$LSB_JOBNAME`	`$SLURM_JOB_NAME`
`$LSB_QUEUE`	`$SLURM_JOB_PARTITION`
`$LSB_SUBCWD`	`$SLURM_SUBMIT_DIR`
`$LSB_DJOB_NUMPROC`	`$SLURM_NTASKS`
`$LSB_HOSTS`	`$SLURM_JOB_NODELIST`

Array syntax¶

Job array specifications in -J "name[1-100]" are converted to separate --job-name=name and --array=1-100 directives.

What it does NOT convert¶

Manual review required

The converter is a starting point, not a complete solution. You must review the output before submitting. The following require manual conversion:

Complex -R resource strings — e.g., rusage[mem=X], span[hosts=1], GPU resource requests. These need to be translated to --mem-per-cpu, --nodes, --gpus, etc. based on your specific needs.
bsub command-line invocations — only #BSUB directives inside scripts are converted, not bsub commands in wrapper scripts or pipelines.
Dependency expressions — -w "done(123) && done(456)" requires manual translation to --dependency=afterok:123:456.
Time format differences — LSF accepts -W 60 (minutes) or -W 1:00 (H:MM). The script converts H:MM to HH:MM:00 but does not convert bare minute values.
Memory unit conversion — LSF -M values are passed through as MB. If your cluster used KB for -M, you'll need to adjust.
Conditional logic using LSF variables — if your script has complex logic around $LSB_* variables beyond simple references, review carefully.

Example¶

Input (myjob.lsf):

#!/bin/bash
#BSUB -J "analysis[1-50]%10"
#BSUB -q normal
#BSUB -W 4:00
#BSUB -n 8
#BSUB -M 16000
#BSUB -o logs/analysis.%J.%I.out
#BSUB -e logs/analysis.%J.%I.err

SAMPLE=$(sed -n "${LSB_JOBINDEX}p" samples.txt)
./process.sh $SAMPLE $LSB_DJOB_NUMPROC

Output:

#!/bin/bash
#SBATCH --job-name=analysis
#SBATCH --array=1-50%10
#SBATCH --partition=normal
#SBATCH --time=04:00:00
#SBATCH --ntasks=8
#SBATCH --mem=16000MB
#SBATCH --output=logs/analysis.%j.%a.out
#SBATCH --error=logs/analysis.%j.%a.err

SAMPLE=$(sed -n "${SLURM_ARRAY_TASK_ID}p" samples.txt)
./process.sh $SAMPLE $SLURM_NTASKS

Converter Script: lsf2slurm.sh¶